3PIZ

Crystal structure of BTK kinase domain complexed with (5-Amino-1-o-tolyl-1H-pyrazol-4-yl)-[3-(1-methanesulfonyl-piperidin-4-yl)-phenyl]-methanone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PIXPDB ENTRY 3PIX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% PEG3350, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.267α = 90
b = 105.304β = 90
c = 38.054γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.24091.60.1359413820
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2861.80.2782.32.1909

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3PIX2.2138.041308969291.430.227590.224930.28164RANDOM40.375
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.88-0.42-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.165
r_dihedral_angle_4_deg23.354
r_dihedral_angle_3_deg14.615
r_dihedral_angle_1_deg5.215
r_scangle_it1.904
r_scbond_it1.185
r_angle_refined_deg1.01
r_mcangle_it0.968
r_mcbond_it0.579
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.165
r_dihedral_angle_4_deg23.354
r_dihedral_angle_3_deg14.615
r_dihedral_angle_1_deg5.215
r_scangle_it1.904
r_scbond_it1.185
r_angle_refined_deg1.01
r_mcangle_it0.968
r_mcbond_it0.579
r_nbtor_refined0.306
r_nbd_refined0.182
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.086
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2017
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms31

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing